/usr/bin/patch-hmm.pl is in snap 2010-07-28-2.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | #!/usr/bin/perl
use strict; use warnings;
die "usage: $0 <hmm> <model> <model> <etc>" unless @ARGV > 1;
my ($hmm, @file) = @ARGV;
my %model;
foreach my $file (@file) {
my $contents = `cat $file`;
my ($type) = $contents =~ /^(\S+)/;
$model{$type} = $contents;
}
open(IN, $ARGV[0]) or die;
while (<IN>) {
print;
last if /SEQUENCE_MODELS/;
}
while (<IN>) {
if (/^(\S+)/) {
my $type = $1;
if (defined $model{$type}) {
print $model{$type};
while (<IN>) {last unless /\S/}
} else {
print;
while (<IN>) {
print;
last unless /\S/;
}
}
}
print;
}
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